Assignment of RFLP linkage groups to their respective chromosomes in aneuploids of sugi (Cryptomeria japonica)

Aneuploids of sugi (Cryptomeria japonica) were found in the open-pollinated progenies of triploidplus tree clones. Seven trisomics and one hypotriploid were used to assign the chromosomes to the RFLP linkage groups constructed previously. The Southern blots containing their genomic DNA were hybridized with the labeled DNA clones corresponding to the loci in the linkage map. The additional dosage in autoradiographs showed that the cloned DNA fragment was located on the extra chromosome in the trisomics. On the other hand, the extra chromosome in two trisomics and the chromosome lacking the triplet in the hypotriploid were cytologically identified as chromosome 10 by consistent presence of a secondary constriction in the proximal region of its short arm. As a result, three linkage groups were assigned to their respective chromosomes, namely chromosome 10 and two other chromosomes.     

Chloroplast DNA in Pinus monticola

Summary Restriction sites on the chloroplast genome of Pinus monticola have been mapped, and the gene for the large subunit of ribulose bisphosphate carboxylase/oxygenase, the genes for the photosystem II polypeptides psbA, psbD and psbC, and the 16S and 23S ribosomal RNA genes have been located. The genome lacks the large inverted repeat characteristic of most angiosperms. The gene order is similar to that found in P. radiata. The presence of dispersed repeated sequences is likely. Two structural features, lack of a large inverted repeat and the presence of dispersed repeats, may confer a degree of variability on the genome which will prove useful in studies of population structure.     

庐山日本柳杉林下穿透雨时空分布特征

林冠是降水到达地面前的第一个作用层,其对降水的再分配作用,导致穿透雨的数量和空间分布具有很大的变异性,这既阻碍了对其的精确评估,也常常被认为是水文模型中蒸发量化的不确定来源之一。在庐山自然保护区日本柳杉(Cryptomeria japonica)人工林内设置了面积30 m×30 m的样地,机械布置了37个截面面积为314.15 cm2穿透雨收集器,于2017年生长季(4—9月)共监测21次降雨事件下穿透雨量。分析林冠下穿透雨率及其时空分布特征和影响因素。日本柳杉林下穿透雨率变化范围为2%—222%,平均穿透雨率为80%,穿透雨率随着林外次降雨量的增加而逐渐增大,降雨量达到28 mm时穿透雨率趋于最大值,之后变化规律复杂未见稳定,二者之间最优拟合关系为二次多项式;与叶面积指数呈显著负相关,叶面积指数小于4.5时对穿透雨率的影响显著。不同叶面积指数下,穿透雨率达到最大时的林外降雨量不同。穿透雨率的空间变异系数的变化范围为15%—114%,随林外降雨量的增加而减小,并在林外次降雨量大于20 mm以后,逐渐趋于稳定,二者之间以对数函数关系式拟合。观测点位的时间变异系数随着叶面积指数的增加而增大。叶面积指数小于5,降雨量小于20 mm时,降雨量是影响穿透雨空间变异性的关键因素。     

The physical map of the chloroplast DNA from Asparagus officinalis L.

The genus Asparagus consists of 100–300 species of both dioecious and hermaphrodite plants. Since there are diploid, tetraploid, and hexaploid plants in this genus, RFLP (restriction fragment length polymorphism) analysis of chloroplast DNA (ctDNA) is suitable for examining the phylogenetic relationships. We have constructed a physical map of the ctDNA of garden asparagus (A. officinalis L. cv Mary Washington 500 W) using five restriction endonucleases, namely, BamHI, PstI, SalI, HindIII, and XhoI. Asparagus ctDNA was digested with restriction enzymes and cloned into plasmid and phage vectors, and a clone bank was constructed that covered 70% of the genome. A physical map was constructed by Southern hybridization of total DNA from asparagus with homologous and heterologous probes. The asparagus ctDNA was about 155 kb long and it contained two inverted repeats (23kb each) separated by a large single-copy region (90kb) and a small single-copy region (19kb). Fifteen genes, encoding photosynthesis-related proteins, rDNAs, and tRNAs, were localized on the physical map of asparagus ctDNA. Comparing the length and the gene order of asparagus ctDNA with that of other plants, we found that asparagus ctDNA was similar to tobacco ctDNA but different from rice ctDNA. The restriction patterns of the ctDNAs from several varieties of A. officinalis and three species of Asparagus were analyzed. The restriction patterns of the varieties of A. officinalis were very similar, but polymorphisms were detected among the three species of Asparagus.     

Formation and vertical distribution of sapwood and heartwood in Cryptomeria japonica D. Don

The formation and vertical distribution of sapwood and heartwood were studied with a 45-year-old Cryptomeria japonica D. Don. The tree was grown at a plantation with 1.5 m × 3.0 m spacing near Miao-Li, Taiwan and was felled on 27 February 1992. The thickness of sapwood and heartwood was expressed by a ring count and a linear measurement. The east-west (E-W) wood strips were collected from 0.3 m above ground upwards to the top of the tree at 2.5 m intervals. The sapwood thicknesses from the base to the 10.3 m tree level height are around 20–22 growth rings and 42±2 mm. At the top of the tree, the sapwood thickness is narrower. The heartwood, which decreases in thickness with increasing tree level heights is not found at the top of the tree. The heartwood appears as a conical shape in the tree trunk. There is no statistical difference in sapwood/heartwood thickness between E-W aspects. Tree level heights and the tree level age were found to be important parameters in determining the thickness of sapwood/heartwood.     

A linkage map for sugi (Cryptomeria japonica) based on RFLP,RAPD, and isozyme loci

A linkage map for sugi was constructed on the basis of restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), and isozyme loci using a three-generation pedigree prepared for genetic analysis of heartwood color. A total of 128 RFLP (123 cDNA and 5 genomic probes), 33 RAPD, 2 isozyme, and 1 morphological (dwarf) loci segregated in 73 progeny. Of the 164 segregating loci, 145 loci were distributed in 20 linkage groups. Of these loci, 91 with confirmed map positions were assigned to 13 linkage groups, covering a total of 887.3 cM. A clustering of markers with distorted segregation was observed in 6 linkage groups. In the four clusters, distortions with a reduction in the number of homozygotes from one parent only were found.Abbreviations MAS marker-assisted selection - PAGE polyacrylamide gel electrophoresis - QTL quantitative traits of loci - RAPD random amplified polymorphic DNA - RFLP restriction fragment length polymorphism This work was supported by a Grant-in-Aid from the Ministry of Agriculture, Forestry and Fisheries of Japan (Integrated Research Program for the Use of Biotechnological Procedures for Plant Breeding) and by a Grant-in-Aid from the Ministry of Education, Science and Culture of Japan (Cooperative Research, no. 04304017)     

Somatic embryogenesis and plant regeneration from immature zygotic embryos of<Emphasis Type="Italic"> Cryptomeria japonica</Emphasis> D. Don

This report describes the successful plant regeneration via somatic embryogenesis from immature zygotic embryos of Cryptomeria japonica D. Don. For the induction of embryogenic tissue, we determined that the optimal medium contained N⁶-benzyladenine and 2,4-dichlorophenoxyacetic acid. Immature zygotic embryos that were collected at the end of June yielded embryogenic tissue at the highest frequency. Embryogenic tissues that had proliferated in liquid medium included small and loosely packed cells and elongating or elongated cells. We used ten cell lines to determine the optimal medium for the development of somatic embryos. Induced somatic embryos germinated with synchronous sprouting of cotyledons, hypocotyls and roots. Gibberellin A₃ in the germination medium had a positive effect on both the elongation of hypocotyls and the survival of seedlings. The frequencies of induction and germination of somatic embryos differed among the cell lines examined. Most of the seedlings grew normally. This system of somatic embryogenesis required 4–5 months for the regeneration of C. japonica plantlets from immature zygotic embryos.Abbreviations ABA Abscisic acid - BA N⁶-Benzyladenine - 2,4-D 2,4-Dichlorophenoxyacetic acid - GA₃ Gibberellin A₃Communicated by F. Sato     

Evidence for involvement of the phenylpropanoid pathway in the biosynthesis of the norlignan agatharesinol

In order to study the biosynthesis of agatharesinol, a norlignan, l-phenylalanine-[ring-2,3,4,5,6-2H] and trans-cinnamic acid-[ring-13C6] were administered to fresh sapwood sticks of Cryptomeria japonica (sugi, Japanese cedar), that is, the labeled precursors were allowed to be absorbed through the tangential section of the wood sticks. The wood sticks were then maintained in high humidity desiccators for approximately 20 d after which ethyl acetate (EtOAc) extracts of the wood sticks were analyzed by gas chromatography-mass spectrometry (GC-MS). Native agatharesinol (trimethylsilylated) produces an m/z 369 ion and an m/z 484 ion that are characteristic of its structure. Agatharesinol formed in the sapwood sticks treated with the deuterium-labeled l-phenylalanine generated both of these ions together with m/z 373 and 377 ions (m/z 369+4 and +8, respectively), and also m/z 488 and 492 ions (m/z 484+4 and +8, respectively). Generation of m/z 373 and 488 ions is attributed to the substitution by deuterium of the four hydrogen atoms of either of the p-hydroxyphenyl rings of agatharesinol, and that of m/z 377 and 492 ions is attributed to the substitution by deuterium of the eight hydrogen atoms of both p-hydroxyphenyl rings. In the administration of the 13C-labeled trans-cinnamic acid, m/z 375 and 381 ions (m/z 369+6 and +12, respectively), and also m/z 490 and 496 ions (m/z 484+6 and +12, respectively) were found, indicating that either aromatic ring or both aromatic rings of agatharesinol were 13C-labeled. Consequently, assimilation of the labeled precursors into agatharesinol was clearly detected, and an experimental procedure for studies on the biosynthesis was developed.     

The Arabidopsis thaliana genome encodes at least four thioredoxins m and a new prokaryotic-like thioredoxin

Screening of cDNA libraries at low stringency and complete sequencing of EST clones with homology to thioredoxins allowed us to characterize five new prokaryotic type Arabidopsis thaliana thioredoxins. All present N-terminal extensions with characteristics of transit peptides. Four are clustered in a phylogenetic tree with the chloroplastic thioredoxin m from red and green algae and higher plants, and their transit peptides have typical characteristics of chloroplastic transit peptides. One is clearly divergent and defines a new prokaryotic thioredoxin type that we have named thioredoxin x. Its transit peptide sequence presents characteristics of both chloroplastic and mitochondrial transit peptides. The five corresponding genes are expressed at different levels, but mostly in green tissues and in in-vitro cultivated cells.     

Chloroplast genome organization of bromegrass,Bromus inermis Leyss

Summary A physical map of the Bromus inermis chloroplast genome was constructed using heterologous probes of barley and wheat chloroplast DNA (cpDNA) to locate restriction sites. The map was aligned from data obtained from filter hybridization experiments on single and double enzyme digests. Cleavage sites for the enzymes PstI, SalI, KpnI, XhoI and PvuII were mapped. The chloroplast genome of B. inermis is similar in physical organization to that of other grasses. The circular cpDNA molecule of B. inermis has the typical small (12.8 kbp) and large (81.3 kbp) single-copy regions separated by a pair of inverted repeat (21 kbp) regions. The cpDNA molecule of B. inermis is collinear in sequence to that of wheat, rye, barley and oats. No structural rearrangements or major deletions were observed, indicating that the cpDNA of Bromus is a useful tool in phylogenetic studies.     

<Emphasis Type="Italic">SulP</Emphasis>, a nuclear gene encoding a putative chloroplast-targeted sulfate permease in<Emphasis Type="Italic"> Chlamydomonas reinhardtii</Emphasis>

Genomic, proteomic, phylogenetic and evolutionary aspects of a novel gene encoding a putative chloroplast-targeted sulfate permease of prokaryotic origin in the green alga Chlamydomonas reinhardtii are described. This nuclear-encoded sulfate permease gene (SulP) contains four introns, whereas all other known chloroplast sulfate permease genes lack introns and are encoded by the chloroplast genome. The deduced amino acid sequence of the protein showed an extended N-terminus, which includes a putative chloroplast transit peptide. The mature protein contains seven transmembrane domains and two large hydrophilic loops. This novel prokaryotic-origin gene probably migrated from the chloroplast to the nuclear genome during evolution of C. reinhardtii. The SulP gene, or any of its homologues, has not been retained in vascular plants, e.g. Arabidopsis thaliana, although it is encountered in the chloroplast genome of a liverwort (Marchantia polymorpha). A comparative structural analysis and phylogenetic origin of chloroplast sulfate permeases in a variety of species is presented.     

Contrasting patterns of genetic diversity in two tropical pines: Pinus kesiya (Royle ex Gordon) and P. merkusii (Jungh et De Vriese)

We studied allozyme and chloroplast (cp) DNA variation in natural populations of Pinus kesiya and P. merkusii from Thailand and Vietnam. The results showed striking differences between the two species in the amount and distribution of allozyme variation. P. kesiya harboured considerable allozyme variation and showed weak interpopulational differentiation. In contrast, P. merkmii had very low intrapopulational variability but a high level of interpopulational differentiation. The average Nei's genetic distance separating the two species was exceptionally high (0.701) taking into account their close taxonomic placement in the same subsection Sylvestres. The constructed phylogenetic trees revealed very early divergence of P. kesiya and P. merkusii. The present analysis of cpDNA variation also confirmed the dissimilar character of these two species and was compatible with other evidence indicating the outstanding position of P. merkusii as compared to other Asian members of the subsection Sylvestres. Analysis of cpDNA variation in sympatric populations of P. kesiya and P. merkusii revealed that they are pure representatives of the species in question. This result indicates that despite an overlapping distribution P. kesiya and P. merkusii do not hybridise in nature. We suggest that the distinctive character of P. merkusii is a result of an early separation from other Eurasian pines. Despite spatial proximity, P. kesiya and P. merkusii are kept apart by strong reproductive barriers. The low genetic variability of P. merkusii may be explained by previous bottlenecks, reduced gene flow among populations, and an inbreeding due to small population size and asynchronous flowering.     

Differences in Mitochondrial Genome Organization of Cryptococcus Neoformans Strains

The organization of the mitochondrial genomes in two strains belonging in different varieties of Cryptococcus neoformans was analysed. Physical maps of the mtDNA of the IFM5844 (var. neoformans) and IFO410 (var. grubii) strains were constructed by using EcoRI and EcoRV restriction enzymes; functional maps were constructed by hybridization, cloning and sequencing. Most of the genes important in the mitochondrial function (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6, ATP9, COX1, COX2 and COB) and protein synthesis (SsrRNA and LsrRNA) were localized. We did not find any differences between the strains in the order of these genes. However, they differed significantly in the sizes of the mtDNAs: 32.6 kb for IFM5844, and 24.1 kb for IFO410. This can be attributed to two large regions of the mtDNA. In these regions, differences were found in the numbers of introns in COX1 (no intron in var. grubii, 5 introns in var. neoformans), COB (1 intron in var. grubii, 2 introns in var. neoformans), LsrRNA (no intron in var. grubii, 2 introns in var. neoformans), and ND5 (no intron in var. grubii, 1 intron in var. neoformans) genes. In several introns of the COB and COX1 genes LAGLIDADG motifs were found. Differences were also observed in the nucleotide sequences of some genes and in the sizes and sequences of intergenic regions. The nucleotide sequences of the genes of the IFM and IFO strains were compared with those of the H-99 and JEC 21 strains from the database. Surprisingly high similarities were found between the strains belonging in var. grubii (IFO 410 and H-99) and var. neoformans (IFM 5844 and JEC 21).     

Nicotiana chloroplast genome III. Chloroplast DNA evolution

Summary Nicotiana chloroplast genomes exhibit a high degree of diversity and a general similarity as revealed by restriction enzyme analysis. This property can be measured accurately by restriction enzymes which generate over 20 fragments. However, the restriction enzymes which generate a small number (about 10) of fragments are extremely useful not only in constructing the restriction maps but also in establishing the sequence of ct-DNA evolution. By using a single enzyme, Sma I, a elimination and sequential gain of its recognition sites during the course of ct-DNA evolution is clearly demonstrated. Thus, a sequence of ct-DNA evolution for many Nicotiana species is formulated. The observed changes are all clustered in one region to form a hot spot in the circular molecule of ct-DNA. The mechanisms involved for such alterations are mostly point mutations but inversion and deficiency are also indicated. Since there is a close correlation between the ct-DNA evolution and speciation in Nicotiana a high degree of cooperation and coordination betwen organellar and nuclear genomes is evident.